Abstract The overall aim is development of noninvasive diffuse Raman tomographic methodology for evaluating the state of bone allografts in a rat model and other problems in bone repair and healing (i.e. microdamage). The applications advance concepts in two areas, including important therapeutic developments in bone graft biology, as well as in the realization of an entirely new type of imaging technology with chemically specific information. The project will consider the optical, biological, imaging, and data reduction aspects of the problem, and the new in vivo imaging technology will be used to study graft success or failure noninvasively. Phantoms with geometries defined by micro-computed tomography (micro-CT) data on rat hind limbs will be used to reproduce bone and overlying tissue geometry accurately. Phantoms will contain gelatin (matrix surrogate), hydroxyapatite (mineral surrogate), lipids, and light absorbing molecules to model both tissue optics and Raman spectra. These phantoms will be used to define and test fiber optic Raman probe geometry, and to assess such problems as motion artifacts. Our candidate Raman probe geometry is circumferential illumination and collection, but other geometries will be considered. Tomographic reconstruction software will be modified for use with low signal/noise ratio Raman data. A new maximum likelihood methodology will be developed for extraction of Raman spectra and calculation of Raman intensities from data sets of remitted Raman-scattered light. Raman band intensity ratios and multivariate statistical parameters will differentiate between newly modeled bone tissue of the rat and the spectroscopically similar allografts. Additional spatial information can be gained using other imaging modalities (MRI, micro-CT). Longitudinal studies in a rat model will be used to assess the ability of this technology to distinguish between allograft tissue and newly modeled bone tissue. Outcome Raman imaging measures of the allograft and microdamage experiments will be correlated with other biomechanical and histochemical techniques.